Table of contents

Changes to cross-references to Ensembl
New event types 'protein splicing' and 'miscellaneous'

Not before: 28-Jul-2009

We have so far cross-referenced the Ensembl database at the level of the gene via Ensembl's gene identifiers. To provide more detailed cross-referencing, we are going to link to Ensembl at the level of gene transcripts and corresponding peptides using Ensembl's transcript and peptide identifiers. This change does not affect the XSD, but may nevertheless require code changes because the gene identifier is moved from the dbReference's id attribute to a property element.

Current format:

<dbReference type="Ensembl" id="ENSG00000104368" key="174">
  <property type="organism name" value="Homo sapiens" />
</dbReference>

New format:

<dbReference type="Ensembl" id="ENST00000220809" key="174">
  <property type="protein sequence ID" value="ENSP00000220809" />
  <property type="gene designation" value="ENSG00000104368" />
  <property type="organism name" value="Homo sapiens" />
</dbReference>
<dbReference type="Ensembl" id="ENST00000270187" key="175">
  <property type="protein sequence ID" value="ENSP00000270187" />
  <property type="gene designation" value="ENSG00000104368" />
  <property type="organism name" value="Homo sapiens" />
</dbReference>
<dbReference type="Ensembl" id="ENST00000270189" key="176">
  <property type="protein sequence ID" value="ENSP00000270189" />
  <property type="gene designation" value="ENSG00000104368" />
  <property type="organism name" value="Homo sapiens" />
</dbReference>
<dbReference type="Ensembl" id="ENST00000352041" key="177">
  <property type="protein sequence ID" value="ENSP00000270188" />
  <property type="gene designation" value="ENSG00000104368" />
  <property type="organism name" value="Homo sapiens" />
</dbReference>

Not before: 01-Sep-2009

Two new event types are going to be added to the comment line topic ALTERNATIVE PRODUCTS in the flat file format of UniProtKB entries. For details of this change, please read the UniProt document Forthcoming changes.

To represent this data in the XML format, we are going to modify the XSD type eventType in the following way:

     <xs:complexType name="eventType">
     ...
         <xs:attribute name="type" use="required">
         ...
                     <xs:enumeration value="protein splicing"/>
                     <xs:enumeration value="miscellaneous"/>